I had to change apdu_masquerade to case4as3 to get Cryptoflex 32k
cards to work (in egate token adapter). I'm not sure if this is a
card issue or a reader driver issue.
Also one small change we did was add a msleep() call to card-flex.c
You could try to remove that line and see if it helps. I needed to
add it for that cryptoflex 32k/ egate combination, and my
normal cryptoflex cards on linux and in other reader still work,
so it shouldn't hurt anyone.
Please let us know if one of these changes solves your problems.